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N-acyl amino acid racemase from Amycolatopsis sp Ts-1-60: G291D F323Y I293G mutant in complex with N-acetyl naphthylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A6G PDB ENTRY 4A6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 100 MM TRIS HCL PH 8; 15% (W/V) PEG 4K; 800 MM SODIUM FORMATE; PROTEIN AT 8 MG PER ML
Crystal Properties Matthews coefficient Solvent content 3.78 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.29 α = 90 b = 217.29 β = 90 c = 262.22 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.58 76.44 99.9 0.13 14.9 12.4 74523 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.65 100 0.84 3 11.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4A6G 2.58 76.44 70766 3755 99.9 0.18074 0.17926 0.1884 0.20834 0.2145 RANDOM 44.079
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.06 -0.03 -0.06 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.079 r_dihedral_angle_4_deg 23.962 r_dihedral_angle_3_deg 17.844 r_dihedral_angle_1_deg 6.341 r_mcangle_it 5.486 r_scbond_it 4.38 r_mcbond_it 3.71 r_mcbond_other 3.71 r_angle_refined_deg 1.757 r_angle_other_deg 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.079 r_dihedral_angle_4_deg 23.962 r_dihedral_angle_3_deg 17.844 r_dihedral_angle_1_deg 6.341 r_mcangle_it 5.486 r_scbond_it 4.38 r_mcbond_it 3.71 r_mcbond_other 3.71 r_angle_refined_deg 1.757 r_angle_other_deg 1.145 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10993 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing